Posts by Cumol

... How do I turn my exon sequences into the fasta format? The only idea I had was to blast them against the target genome (using ensembl) and then convert the output into GTF. But it doesn't seem to be so straight forward.
Is there a better option? ...

... What is the best way to edit the GTF file?
Would I remove the lines associated with the Gene I am interested in and then add my custom lines?
I will probably need the exact start and end of each exon on the genome I am using for indexing, right? ...

... A recent publication investigated splice variants of a gene I am interested in (using SMRT seq) and they described different/additional exons compared to what I find in NCBI or ENSEMBL.
I wanted to analyze splice variants and exon counts of this gene using the described exons from this publication ...

... Does not seem to work for me using this:
> library(biomaRt)
>listMarts(host = "asiadb.ensembl.org", port = 5306)
I get the error:
>Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is temporarily down. Check ...